Sparse regression, classification, and microbial network estimation in QIIME2 with q2-classo and q2-gglasso

TL;DR

This paper introduces two new QIIME 2 plugins, q2-classo and q2-gglasso, for penalized regression, classification, and microbial network estimation tailored to high-dimensional, compositional microbiome data.

Contribution

The paper presents novel plugins for QIIME 2 that enable sparse regression, classification, and network modeling specifically designed for microbial compositional data.

Findings

Demonstrated robust model selection and classification on Atacama soil microbiome data.

Enabled estimation of microbial association networks using sparse graphical models.

Decomposed taxon-taxon associations into direct interactions and latent factors.

Abstract

Motivation: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce. Results: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors. Availability: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.